An example document

An HTML example

A standard workflow

A Quarto workflow

Solution: Use a Quarto workflow everything (code, text, metadata) in one place. Let Quarto do the magic

The basic Quarto workflow

1. Create a .qmd document

Step 1 - Create the document

Open R Studio and go to File -> New File -> Quarto Document

Just click Create and the file will open in R Studio.

In other environments you can just create and empty file with .qmd ending

The basic Quarto workflow

• text e.g. introduction, methods, or discussion
• code (R, Python, Julia) that produces numbers, figures, tables, …
• metadata that defines how the document should look like (e.g. which output format)

3. Render the document to a defined output format (e.g. PDF) using Quarto

Step 3 - Render the document

References for all the elements

The text body - Markdown

Markdown is a simple markup language to create formatted text, you can e.g.

# Header level 1
## Header level 2
### Header level 3

A bullet point list

- item 1
- item 2
- item 3

The text body - Markdown

You can also do more complex things like:

• Including images, links or footnotes
• Adding citations
• Latex style mathematical formulas

The text body - Markdown

If you don’t want to use markdown, there is a really nice feature in R Studio: The visual editor.

The visual editor in R Studio

Convenient, word-like interface for formatting text and adding features.

The visual editor in R Studio

Using the visual editor, makes many things that would be painful in Markdown really easy.

My favorite feature in the visual editor:

• Add citations (Insert -> Citation) from Zotero library, DOI search, PubMed, …

The Code

Code can be included in code chunks or as inline code

The Code

Inline code starts and ends with 1 backtick

`r `

The mean of the values 1, 2 and 3 is `r mean(1:3)`

The Code

Code chunks starts and ends with 3 backticks

```{r}
library(ggplot2)

ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess")
```

```{python}
import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(subplot_kw = {'projection': 'polar'})
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```

The Code

Insert a code chunk (R Studio)

The Code

Run code chunk

• Code chunks are run when document is rendered
• Code chunks can also be run like “normal” code
• Run Code chunk by clicking on the green arrow next to the chunk

The code

Code chunk have special comments that start with #| and that control the behaviour of the chunk.

```{r}
#| label: fig-airquality
#| fig-cap: Temperature and ozone level.
#| include: false

library(ggplot2)

ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess")
```

• label: Figure and chunk label that can be referred to in text
• fig-cap: Figure caption
• include: Include the output (i.e. the plot) in the document but don’t show the code

YAML header

---
title: "My first document"
subtitle: "Whatever subtitle makes sense"
author: "Selina Baldauf"
date: "`r Sys.Date()`"
---

YAML header

For document output formats

---
title: "My first document"
author: "Selina Baldauf"
date: "`r Sys.Date()`"
format: html
---

---
title: "My first document"
author: "Selina Baldauf"
date: "`r Sys.Date()`"
format: 
  html: default
  pdf: default
  docx: default
---

YAML header

Execute options

• Default options for code chunks
• Can be overwritten by local comments in code chunks

---
title: "My first document"
author: "Selina Baldauf"
date: "`r Sys.Date()`"
format: html
execute: 
  message: false
  warning: false
---

Summary

• Quarto combines formatted text and code to create reproducible documents

Outlook

Outlook

Quarto offers many more things like:

• Presentations (Powerpoint or Revealjs/HTML)
• Websites
• Easily publish your documents or websites on quartopub or Github
  • See here for more information
• Control the rendering process via R scripts using quarto::quarto_render()
• Parameterized reports

Next lecture

Thank you for your attention :)

Questions?